Supplementary Figure 6: Validation of scRNA-seq and sc-itChIP-seq data of Nkx2-5 cardiac cell lineages from E7.75 and E8.25 hearts.

a, Pseudotime analysis showing two trajectories of cardiomyocyte (CM) and endothelial cell (EC) lineage starting from cardiac progenitor cell population (CP) at E7.75 and E8.25. Single cells were from two biologically independent experiments. b, Scatter plot showing the marker gene expression of single cells over the developmental pseudotime. Three representative marker genes in each row were selected for the cell type validation of EC, CM and CP respectively. c, Heatmap showing H3K27ac signals around the housekeeping genes. The columns represent single cells as ordered in Fig. 6f. Single cells were from two biologically independent experiments. The housekeeping gene lists are from the studies by Dix et al.³⁰. and De Jonge et al.²⁹. d, Scatter plot showing the H3K27ac signals at two representative housekeeping gene regions on tSNE as in Fig. 6e. Single cells were from two biologically independent experiments. e, Pseudotime analysis showing two trajectories of cardiomyocyte (CM) and endothelial cell (EC) lineage starting from cardiac progenitor cell population (CP) at E7.75 and E8.25. Single cells were from two biologically independent experiments. f, Scatter plot showing H3K27ac signals at peak regions nearby feature genes in single cells of CM and EC lineages corresponding to Fig. 6e. H3K27ac signals were calculated by counting the reads at peak regions and then normalized by read depth. g, A full heatmap of all clusters showing the normalized H3K27ac signals of three “pseudocells” (CP, EC and CM) as in Fig. 6g at peak regions, related to Fig. 6h. Peaks were clustered into 4 groups by K-means. C1, C2 and C3 were positively correlated with CP, CM and EC respectively, and C4 was the negatively correlated peaks. Of note, no signals were detected in a large number of regions (rows), probably due to the fact that those are enriched in other single cells rather than from the ending cell populations analyzed here.